Genetic analysis of the single internode dwarf 1 mutant in barley
Abstract Background Stem development is crucial for plant lodging, nutrients and water transport, and structural support for other organs. Understanding stem development and growth is essential for ensuring global food security. Although numerous lodging-resilient and high-yielding crop varieties ha...
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| Language: | English |
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BMC
2025-07-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06790-6 |
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| author | Megan Overlander-Chen Jason D. Fiedler Shaobin Zhong Shengming Yang |
| author_facet | Megan Overlander-Chen Jason D. Fiedler Shaobin Zhong Shengming Yang |
| author_sort | Megan Overlander-Chen |
| collection | DOAJ |
| description | Abstract Background Stem development is crucial for plant lodging, nutrients and water transport, and structural support for other organs. Understanding stem development and growth is essential for ensuring global food security. Although numerous lodging-resilient and high-yielding crop varieties have been developed in the Green Revolution by controlling plant height, the molecular mechanism underlying stem development, particularly for cereals, is not fully understood. The allelic stem mutants in barley (Hordeum vulgare subsp. vulgare), single internode dwarf 1 (sid1), provide a model system for genetic studies on stem development. Results We characterized and genetically analyzed the sid1.b mutation. To determine the precise position of Sid1, a high-resolution genetic map was constructed. Segregating F2 plants derived from a cross between wild type (WT) and the mutant were genotyped with the barley 50 k iSelect SNP Array, and the detected SNPs were converted to PCR-based markers for fine mapping. The Sid1 gene was mapped to a 429-kb region on chromosome 4H. Illumina sequencing of WT and sid1 identified a C → T transition in an epidermal pattern factor (EPF)-coding gene, which introduces a premature stop codon in the mutant allele. Conclusions In the present study, we genetically characterized and mapped the sid1.a mutation, which causes a dwarfed phenotype with single internode stems in barley. The EPF-encoding gene in the delimited region is a promising candidate for Sid1. Therefore, our study provides a foundation for cloning of Sid1, which will enhance our understanding of the molecular mechanisms underlying stem development, particularly in monocot plants. |
| format | Article |
| id | doaj-art-e8b0b9efb4a8494e9dd76e0d89c4613e |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-e8b0b9efb4a8494e9dd76e0d89c4613e2025-08-20T03:37:23ZengBMCBMC Plant Biology1471-22292025-07-012511910.1186/s12870-025-06790-6Genetic analysis of the single internode dwarf 1 mutant in barleyMegan Overlander-Chen0Jason D. Fiedler1Shaobin Zhong2Shengming Yang3USDA-ARS Cereals Research Improvement Unit, Edward T. Schafer Agriculture Research CenterUSDA-ARS Cereals Research Improvement Unit, Edward T. Schafer Agriculture Research CenterUSDA-ARS Cereal Disease LaboratoryUSDA-ARS Cereals Research Improvement Unit, Edward T. Schafer Agriculture Research CenterAbstract Background Stem development is crucial for plant lodging, nutrients and water transport, and structural support for other organs. Understanding stem development and growth is essential for ensuring global food security. Although numerous lodging-resilient and high-yielding crop varieties have been developed in the Green Revolution by controlling plant height, the molecular mechanism underlying stem development, particularly for cereals, is not fully understood. The allelic stem mutants in barley (Hordeum vulgare subsp. vulgare), single internode dwarf 1 (sid1), provide a model system for genetic studies on stem development. Results We characterized and genetically analyzed the sid1.b mutation. To determine the precise position of Sid1, a high-resolution genetic map was constructed. Segregating F2 plants derived from a cross between wild type (WT) and the mutant were genotyped with the barley 50 k iSelect SNP Array, and the detected SNPs were converted to PCR-based markers for fine mapping. The Sid1 gene was mapped to a 429-kb region on chromosome 4H. Illumina sequencing of WT and sid1 identified a C → T transition in an epidermal pattern factor (EPF)-coding gene, which introduces a premature stop codon in the mutant allele. Conclusions In the present study, we genetically characterized and mapped the sid1.a mutation, which causes a dwarfed phenotype with single internode stems in barley. The EPF-encoding gene in the delimited region is a promising candidate for Sid1. Therefore, our study provides a foundation for cloning of Sid1, which will enhance our understanding of the molecular mechanisms underlying stem development, particularly in monocot plants.https://doi.org/10.1186/s12870-025-06790-6Sid1Stem developmentGenetic mappingBarley |
| spellingShingle | Megan Overlander-Chen Jason D. Fiedler Shaobin Zhong Shengming Yang Genetic analysis of the single internode dwarf 1 mutant in barley BMC Plant Biology Sid1 Stem development Genetic mapping Barley |
| title | Genetic analysis of the single internode dwarf 1 mutant in barley |
| title_full | Genetic analysis of the single internode dwarf 1 mutant in barley |
| title_fullStr | Genetic analysis of the single internode dwarf 1 mutant in barley |
| title_full_unstemmed | Genetic analysis of the single internode dwarf 1 mutant in barley |
| title_short | Genetic analysis of the single internode dwarf 1 mutant in barley |
| title_sort | genetic analysis of the single internode dwarf 1 mutant in barley |
| topic | Sid1 Stem development Genetic mapping Barley |
| url | https://doi.org/10.1186/s12870-025-06790-6 |
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